ISLAMABAD — A leading coalition of American humanitarian aid groups has written to the CIA chief to protest the agency's use of a Pakistani doctor to help track Osama bin Laden, linking the ploy to a worsening polio crisis in Pakistan.

Polio, a crippling childhood disease, is endemic now in only three countries, including Pakistan, which had the highest number of polio cases in the world last year. Health workers in this impoverished nation warn of a health catastrophe could spiral out of control.

Last July, McClatchy revealed that the CIA had instructed a Pakistani doctor, Shakil Afridi, to set up a fake vaccination scheme in the Pakistani town of Abbottabad to gain entry to the house where it suspected that bin Laden was living. The goal of the scheme was to extract DNA samples from the al Qaida chief's family members.

But to many Pakistanis, the ruse seemingly provided proof for a widely believed prejudice — fueled by religious extremists — that vaccinations, especially polio drops, are a Western conspiracy to sterilize Muslims.

"The CIA's use of the cover of humanitarian activity for this purpose casts doubt on the intentions and integrity of all humanitarian actors in Pakistan, thereby undermining the international humanitarian community's efforts to eradicate polio, provide critical health services and extend life-saving assistance during times of crisis, like the floods seen in Pakistan over the last two years," the coalition of aid agencies, InterAction, wrote in its letter to CIA director David Petraeus.

The alliance of 200 American nongovernmental organizations said the CIA's tactics also had endangered the lives of foreign aid workers.

In recent months, presumed Islamic extremists have kidnapped at least five international employees of nongovernmental organizations, including an American, Warren Weinstein. Pakistani intelligence agents have increased surveillance and harassment of foreign aid workers since the Afridi saga, according to InterAction and interviews McClatchy has conducted.

A poor country of 180 million people, Pakistan desperately needs foreign assistance for its humanitarian needs, including dealing with the aftermath of massive flooding in 2010 and 2011.

"The CIA-led immunization campaign compromises the perception of U.S. NGOs as independent actors focused on a common good and casts suspicion on their humanitarian workers. The CIA's actions may also jeopardize the lives of humanitarian aid workers in Pakistan," InterAction's letter said.

The American agencies, which include the International Rescue Committee, Mercy Corps and CARE, reacted after Defense Secretary Leon Panetta in January publicly acknowledged Afridi's role in the bin Laden hunt for the first time.

Joel Charny, a vice president at InterAction, said in an interview that Panetta's remarks to CBS provided the opportunity to raise the issue with the letter, which the alliance faxed to Petraeus on Feb. 21. InterAction said it hadn't received a reply.

"We're not trying to embarrass anyone," Charny said. "But we can't have bogus humanitarian activities going on in the name of national security."

"The vaccination effort was limited and real. It was conducted by genuine medical professionals who planned to provide everyone with the full course of treatments," a senior U.S. official told McClatchy, speaking only on the condition of anonymity due to a lack of authorization to talk to journalists. "The idea that this was in any way a `fake' public health effort is simply mistaken. If the effort had not been interrupted by arrests, many Pakistani children would have been fully immunized.

"The doctor was never asked to spy on Pakistan — he was asked only to help locate the most wanted terrorist in the world. The other dedicated medical professionals who conducted the vaccination campaign with the doctor were not involved in the effort to confirm bin Laden's presence."

Before the U.S. raid last May 2 that killed bin Laden, the CIA was unsure whether the al Qaida chief was really living in Abbottabad. Afridi used nurses to go house-to-house in the town to provide hepatitis vaccinations, and managed to gain entry to the compound where bin Laden was suspected to be living but apparently failed to get the DNA.

The idea may have come from the fact that a nurse previously had managed to get into the bin Laden compound to administer polio drops to his children and grandchildren.

Polio has staged a startling comeback in Pakistan since 2005. Last year, nearly 200 Pakistani children were paralyzed by the disease, accounting for 60 percent of all new polio cases worldwide, according to the United Nations Children's Fund.

The situation is worst in the tribal area, along the Afghan border, and the remote western province of Baluchistan, the least educated parts of the country. The outbreak could lead to other countries slapping travel restrictions on Pakistani citizens.

Washington has been pressuring Pakistan to release Afridi, whom Pakistani authorities arrested some three weeks after the bin Laden raid. This week, Secretary of State Hillary Clinton said Pakistan had "no basis" for holding him.

While U.S. officials may regard Afridi as a hero for helping to track the world's most wanted terrorist, Pakistan, which was humiliated by the bin Laden operation, thinks that Afridi has committed treason by working for a foreign intelligence agency.

Abdul Basit, a spokesman for Pakistan's Ministry of Foreign Affairs, told McClatchy that Afridi "is being dealt with in accordance with our law. We expect all to respect our legal process, and refrain from making insinuations and drawing premature conclusions."

(Shah is a McClatchy special correspondent. Jonathan S. Landay contributed to this article from Washington.)

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